Extract and Visualize Pangenome Information ℹ️#

The info subcommand extracts summary information from PPanGGOLiN .h5 pangenome files and generates interactive HTML reports. These reports support quick content comparison of each pangenome.

Info command line usage ️#

panorama info -i <pangenome_list.tsv> -o <output_directory> [--status] [--content]

Output#

status_info.html — Status of pangenome processing steps (annotation, clustering, etc.)
content_info.html — Numerical summary: genomes, genes, gene families, modules, etc.

Key options#

Option	Description
–status	Extract and export the status (booleans) of each pangenome.
–content	Extract and export structural and numerical content metrics.

default If no flags are provided, all (status, content, parameters, metadata) are extracted.

Warning

--parameters and --metadata outputs are not settled yet. We are currently working on a useful output. Please add --status and/or --content to don’t get an error.

Exploring the Reports#

Status info#

Shows whether each processing step was completed:

Example columns: Genomes_Annotated, Genes_Clustered, RGP_Predicted, etc.

Features:

Radio button filters for boolean values.
TSV download of filtered results.

Content info#

Displays statistics such as:

Number of genes, genomes, gene families, modules.
Frequencies and standard deviations.
Partition composition (persistent, shell, cloud).